IGFL3

protein-coding

IGF like family member 3, the group of IGF like family

Gene summary

IGFL3 belongs to the insulin-like growth factor (IGF; see MIM 147440) family of signaling molecules that play critical roles in cellular energy metabolism and in growth and development, especially prenatal growth (Emtage et al., 2006 [PubMed 16890402]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_207393.2

Inheritance

—

ClinVar variants

U:23B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr19:46,120,067-46,124,688

External References & Databases

Ensembl (ENSG00000188624)

Transcript & Mutation Effects

hg38 • Region Span ~4.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IGFL3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 24

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207393.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			23 clinvar	1 clinvar		24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	1	0	24

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207393.2	RefSeq	NP_997276.1	4	MANE Select
ENST00000341415.3	Ensembl	ENSP00000344860.2	4	MANE Select
ENST00001066478.1	Ensembl	ENSP00000736284.1	3	Standard
ENST00001141866.1	Ensembl	ENSP00000808158.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

signaling receptor binding

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341415
Coding exons: 4
Length: 4604
Individuals with no LoFs: 125492
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125509
p: 0.0000677

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.147	67	70.5	0.951	0.00000384	796
Missense (PolyPhen)		31	30.692	1.01		362
Synonymous	-0.567	31	27.2	1.14	0.00000143	240
Loss of Function	1.25	4	7.77	0.515	4.28e-7	85

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000055	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Potential ligand of the IGFLR1 cell membrane receptor. {ECO:0000269|PubMed:21454693}.;

Intolerance Scores

LoFtool: 0.689
RVIS EVS: 0.37
RVIS percentile EVS: 74.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.144

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium